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Species Identification and Habitat Assessment of the South Texas Siren

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Species Identification and Habitat Assessment of the South Texas Siren University of Texas Rio Grande Valley ScholarWorks @ UTRGV UTB/UTPA Electronic Theses and Dissertations Legacy Institution Collections 7-2015 Species Identification and Habitat Assessment of the South Texas Siren Taylor C. LaFortune The University of Texas Rio Grande Valley Follow this and additional works at: https://scholarworks.utrgv.edu/leg_etd Part of the Animal Sciences Commons, and the Biology Commons Recommended Citation LaFortune, Taylor C., "Species Identification and Habitat Assessment of the South exasT Siren" (2015). UTB/UTPA Electronic Theses and Dissertations. 4. https://scholarworks.utrgv.edu/leg_etd/4 This Thesis is brought to you for free and open access by the Legacy Institution Collections at ScholarWorks @ UTRGV. It has been accepted for inclusion in UTB/UTPA Electronic Theses and Dissertations by an authorized administrator of ScholarWorks @ UTRGV. For more information, please contact [email protected], [email protected]. Species identification and habitat assessment of the South Texas siren A Thesis Presented to the Faculty of the College of Science, Mathematics, and Technology The University of Texas at Brownsville In Partial Fulfillment Of the Requirements for the Degree Master of Science By Taylor Courtney LaFortune July 2015 Copyright By Taylor Courtney LaFortune July 2015 ACKNOWLEDGEMENTS Thank you to the Texas Parks and Wildlife Department for funding this thesis research. First and foremost, I would not have been able to complete this project without the knowledge, guidance, and support of my advisor Dr. Richard J. Kline. I would also like to thank my committee member Dr. Daniele Provenzano at The University of Texas at Brownsville for his encouragement, advice, and humor throughout the entire process, and Dr. Andrew Gluesenkamp at Texas Parks and Wildlife for his insightfulness and direction. A special thanks also goes to Dr. Gluesenkamp, Dan Saenz, Travis LaDuc, Heidi Smith-Parker and Paul Moler for providing tissue samples. I appreciate the help of all the volunteers, especially Kristen Kline, Maria Cooksey, and Crystal Lopez, for their constant willingness and enthusiasm for assisting with field work during the summer heat in Texas, and Connie Mata, who spent long days and nights working in the laboratory. Without the support of my friends and volunteers, this research would not have been possible. I would also like to thank the numerous land owners, state park officials, and the US Fish and Wildlife agency for assisting me with the permits and study sites for conducting my fieldwork. Lastly, I would whole-heartedly like to thank my parents, Marc and Ann LaFortune, my sisters, Andrea LaFortune and Marquis Stakes, and Adam Duffek, for their constant love, advice, and unwavering support. iii LaFortune, T.C., “Species identification and habitat assessment of the South Texas siren.” Unpublished Master of Biology Thesis, The University of Texas at Brownsville, Brownsville, TX, 2015. ABSTRACT At least one species of siren is endemic to the Rio Grande Valley of Texas, yet very little is known about the populations of the region. Texas Parks and Wildlife refers to the populations of Siren spp. in South Texas as the “South Texas siren (large form Siren sp. 1),” and recognizes these populations as a threatened species, yet their current population status remains unclear. The species identification of the South Texas siren has been hampered by similarity in morphology across species, and by the lack of complete siren genetic sequences in the NCBI GenBank database. In addition to species ambiguity, very little is known about the preferred habitat characteristics of sirens, specifically in South Texas. The aim of this study was to identify the species of Siren spp. that inhabit South Texas, and to assess the vegetation and environmental variables of siren habitat. Sirens were collected from seventeen water bodies throughout South Texas. Thirty-six sites were assessed for siren presence and correlation with environmental variables, co- occurring species, and vegetation composition. There was no significant correlation between siren presence and the environmental factors; however, nearly all sirens were collected in water bodies that had a high (>95%) percent cover of edge vegetation, and siren abundance appeared to be affected by seasonality. A total of 65 South Texas siren tissue samples were collected between 2013 and 2015. Confirmed specimens of Siren lacertina were compared with the South Texas siren samples, to analyze both coding and non-coding regions (protein coding genes, rRNAs, and tRNAs). For species identification, nine complete mitochondrial genomes were sequenced, and comparisons were made against single genes to assess their utility for species resolution. Sequence divergence and phylogenetic relationships suggest that siren populations in South Texas are composed of at least one distinct species that differs from published sequences for Siren intermedia and S. lacertina. In addition, the results suggest that CO1 is likely the most useful gene for species identification in lieu of the complete mitochondrial genome. The results from this study will provide critical information for this cryptic species, and will aid in the development of future conservation and management practices. iv Table of Contents ACKNOWLEDGEMENTS ........................................................................................... III ABSTRACT ..................................................................................................................... IV TABLE OF CONTENTS ................................................................................................ V LIST OF TABLES ........................................................................................................ VII LIST OF FIGURES ..................................................................................................... VIII LIST OF ABBREVIATIONS ........................................................................................ XI I. INTRODUCTION ......................................................................................................... 1 AMPHIBIAN DECLINE ........................................................................................................ 1 GENUS SIREN .................................................................................................................... 3 Habitat ......................................................................................................................... 3 Seasonality ................................................................................................................... 6 Distribution .................................................................................................................. 8 SPECIES IDENTIFICATION .................................................................................................. 9 Mitochondrial DNA ................................................................................................... 10 OBJECTIVES AND HYPOTHESES ...................................................................................... 14 II. MATERIALS AND METHODS .............................................................................. 16 STUDY SITES .................................................................................................................. 16 TRAP COLLECTIONS AND ENVIRONMENTAL VARIABLES ................................................ 16 PHOTO-ID ...................................................................................................................... 19 SAMPLE COLLECTION ..................................................................................................... 20 HABITAT ANALYSIS ....................................................................................................... 20 Co-occurring Species Composition ........................................................................... 20 Vegetation Composition ............................................................................................ 21 MTDNA ANALYSIS ........................................................................................................ 22 DNA extraction, cloning, and sequencing ................................................................. 22 Sequence Assembly .................................................................................................... 24 Sequence Alignments ................................................................................................. 25 PHYLOGENETIC ANALYSIS ............................................................................................. 26 Bayesian Analyses ..................................................................................................... 26 Maximum Likelihood Analyses .................................................................................. 28 Sequence Divergence Analyses ................................................................................. 28 III. RESULTS .................................................................................................................. 31 v SIREN COLLECTION DATA .............................................................................................. 31 WILD-ID ........................................................................................................................ 32 HABITAT DATA .............................................................................................................
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